December 10, 2012

On the South Asian (?) ancestry of Daniel MacArthur

Razib investigates an unexpected region of South Asian admixture in Daniel MacArthur of GenomesUznzipped, and wonders why this has never been found before, despite the fact that his data was out in the public for a while.

I was surprised about this myself, since I had studied this data when I was starting my ADMIXTURE experiments a couple of years ago. But looking back at that old experiment, it's immediately clear why Dr. MacArthur's column (highlighted) showed no evidence of South Asian admixture at the time: there was no South Asian ancestral population in that reference set!

Naturally, I was curious to see what would turn up if I ran this sample again through my most recent globe13 calculator, which I did using the "bychr" mode of DIYDodecad, which treats each of the 22 autosomes separately:

A clear outlier is indeed shown on chr10 which shows 20.51% "South_Asian" admixture; most of the other chromosomes lack this altogether, so this seems like a legitimate signal of admixture.

I next used the "byseg" mode of DIYDodecad in order to (i) localize this admixture signal within chr10 and study it further. Furthermore, I used the paint_byseg script in order to show how the top-4 components within chr10 varied along the length of the chromosome:

It does appear that a good portion of the first half of chr10 has "South_Asian" ancestry, with the signal close to ~50%, which is a fairly good indication that one half of the diploid genome in this region has this type of ancestry.

Interestingly, the South_Asian signal does not appear "constant" along this portion, but in some of its troughs, the "West_Asian" component shows a corresponding local peak. Now, this might be the case of one really long segment of ancestry which is interpreted sometimes as South_Asian, sometimes as West_Asian by the software, given that the South_Asian component inferred by ADMIXTURE is a composite of West_Asian-like Ancestral North Indians (ANI), and Ancestral South Indians (ASI). But, we can investigate this further by using globe4, which looks at the same chromosome at a lower level of resolution:

It does appear to me that a fairly convincing "Asian" signal exists in a good portion of this region. Note that "Asian" within the context of globe4 is a combination of East/South Eurasians and even Australasians; it is a generalized "Asian" component that captures some of the common ancestry of these populations.

So, on balance I would say that there does indeed appear to evidence of South Asian ancestry within chr10 for this sample, and, moreover, this type of South Asian ancestry is probably partly ASI-related.

7 comments:

I think there are 2 possibilities to the 1.5% "South Asian", as follows:

1. One of Dan's ancestors was a British Army soldier in India, who settled with his "native" wife in Australia on retirement - this is the case with a relative of mine, so I'd rate this somewhat likely.2. One of Dan's ancestors was a convict, who escaped into the Bush and married an Australian Aboriginal - I'd rate this much more likely.

Maybe others who have some minor Aboriginal ancestry can chime in, and tell us if it shows up as South Asian.

My Mom turned up a mysterious South Asian segment (one strand, ~18cM) on the X chromosome chromosome in Doug McDonalds analysis. Odd given she has a good tree with everyone from a small inland country area (in England).

I think it is pre 17th century Roma. Sailors and foreigners are very unlikely given they were relatively isolated country farmers. A Roma visiting the local fair or doing seasonal work, who settles down to stay, is entirely beleivable.

If we are speculating, I would say, one of his Australian ancestors had an "Afghan" ancestor, one of those folk brought to Australia to move goods, food and mail by camel to remote inland settlements. The "Afghans" came from Pakistan and Afghanistan.

I've been convinced by you and Razib that this is real - now digging into the source. I have a great-great-great-grandfather on my paternal side who served in India for 15 years, so there were certainly opportunities for admixture...

If you want to pursue this further, you might be interested to know that Family Tree DNA (FTDNA) has a project for exactly this:http://www.familytreedna.com/public/fibis/default.aspx

One thing you'll note in this project is that although the surnames are Irish/British and the Y-DNA is Western Europe, quite a few of the mtDNA samples indicate a South Asian origin:http://www.familytreedna.com/public/fibis/default.aspx?section=mtresults

This project is related to the "Families in British India Society", whose website is here:http://www.new.fibis.org/

Who have a searchable online database, here:http://search.fibis.org/frontis/bin/

When I searched for "MacArthur", I got 33 hits, some in Bombay, Bengal and Madras...

When I search the "Scots Brigade Muster Roll 1804", there is a:Peter McArthur - Assistant Surgeon

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